Tuesday, June 30, 2009

Plants or meat: That's about all that fossils ever tell paleontologists about a dinosaur's diet. But the skull characteristics of a new species of parrot-beaked dinosaur and its associated gizzard stones indicate that the animal fed on nuts and/or seeds. These characteristics present the first solid evidence of nut-eating in any dinosaur.

"The parallels in the skull to that in parrots, the descendants of dinosaurs most famous for their nut-cracking habits, is remarkable," said Paul Sereno, a paleontologist at the University of Chicago and National Geographic Explorer-in-Residence. Sereno and two colleagues from the People's Republic of China announce their discovery June 17 in the Proceedings of the Royal Society B.

The paleontologists discovered the new dinosaur, which they've named Psittacosaurus gobiensis, in the Gobi Desert of Inner Mongolia in 2001, and spent years preparing and studying the specimen. The dinosaur is approximately 110 million years old, dating to the mid-Cretaceous Period.

The quantity and size of gizzard stones in birds correlates with dietary preference. Larger, more numerous gizzard stones point to a diet of harder food, such as nuts and seeds. "The psittacosaur at hand has a huge pile of stomach stones, more than 50, to grind away at whatever it eats, and this is totally out of proportion to its three-foot body length," Sereno explained.

Technically speaking, the dinosaur is also important because it displays a whole new way of chewing, which Sereno and co-authors have dubbed "inclined-angle" chewing. "The jaws are drawn backward and upward instead of just closing or moving fore and aft," Sereno said. "It remains to be seen whether some other plant-eating dinosaurs or other reptiles had the same mechanism."

The unusual chewing style has solved a major mystery regarding the wear patterns on psittacosaur teeth. Psittacosaurs sported rigid skulls, but their teeth show the same sliding wear patterns as plant-eating dinosaurs with flexible skulls.

By using a super-computer to virtually squeeze and heat iron-bearing minerals under conditions that would have existed when the Earth crystallized from an ocean of magma to its solid form 4.5 billion years ago, two UC Davis geochemists have produced the first picture of how different isotopes of iron were initially distributed in the solid Earth.

The discovery could usher in a wave of investigations into the evolution of Earth’s mantle, a layer of material about 1,800 miles deep that extends from just beneath the planet’s thin crust to its metallic core.

"Now that we have some idea of how these isotopes of iron were originally distributed on Earth,” said study senior author James Rustad, a chancellor’s fellow and professor of geology, “we should be able to use the isotopes to trace the inner workings of Earth’s engine.”

A paper describing the study by Rustad and co-author Qing-zhu Yin, an associate professor of geology, was posted online by the journal Nature Geoscience on Sunday, June 14, in advance of print publication in July.

Sandwiched between Earth's crust and core, the vast mantle accounts for about 85 percent of the planet's volume. On a human time scale, this immense portion of our orb appears to be solid. But over millions of years, heat from the molten core and the mantle’s own radioactive decay cause it to slowly churn, like thick soup over a low flame. This circulation is the driving force behind the surface motion of tectonic plates, which builds mountains and causes earthquakes.

One source of information providing insight into the physics of this viscous mass are the four stable forms, or isotopes, of iron that can be found in rocks that have risen to Earth’s surface at mid-ocean ridges where seafloor spreading is occurring, and at hotspots like Hawaii’s volcanoes that poke up through the Earth’s crust. Geologists suspect that some of this material originates at the boundary between the mantle and the core some 1,800 miles beneath the surface.

“Geologists use isotopes to track physico-chemical processes in nature the way biologists use DNA to track the evolution of life,” Yin said.

Because the composition of iron isotopes in rocks will vary depending on the pressure and temperature conditions under which a rock was created, in principle, Yin said, geologists could use iron isotopes in rocks collected at hot spots around the world to track the mantle’s geologic history. But in order to do so, they would first need to know how the isotopes were originally distributed in Earth’s primordial magma ocean when it cooled down and hardened.

As a team, Yin and Rustad were the ideal partners to solve this riddle. Yin and his laboratory are leaders in the field of using advanced mass spectrometric analytical techniques to produce accurate measurements of the subtle variations in isotopic composition of minerals. Rustad is renowned for his expertise in using large computer clusters to run high-level quantum mechanical calculations to determine the properties of minerals.

The challenge the pair faced was to determine how the competing effects of extreme pressure and temperature deep in Earth’s interior would have affected the minerals in the lower mantle, the zone that stretches from about 400 miles beneath the planet’s crust to the core-mantle boundary. Temperatures up to 4,500 degrees Kelvin in the region reduce the isotopic differences between minerals to a miniscule level, while crushing pressures tend to alter the basic form of the iron atom itself, a phenomenon known as electronic spin transition.

Using Rustad’s powerful 144-processor computer, the two calculated the iron isotope composition of two minerals under a range of temperatures, pressures and different electronic spin states that are now known to occur in the lower mantle. The two minerals, ferroperovskite and ferropericlase, contain virtually all of the iron that occurs in this deep portion of the Earth.

These calculations were so complex that each series Rustad and Yin ran through the computer required a month to complete.

In the end, the calculations showed that extreme pressures would have concentrated iron’s heavier isotopes near the bottom of the crystallizing mantle.

It will be a eureka moment when these theoretical predictions are verified one day in geological samples that have been generated from the lower mantle, Yin said. But the logical next step for him and Rustad to take, he said, is to document the variation of iron isotopes in pure chemicals subjected to temperatures and pressures in the laboratory that are equivalent to those found at the core-mantle boundary. This can be achieved using lasers and a tool called a diamond anvil.

Scientists have found that a small Hawaiian squid can hide itself by using an organ with the same genes found in its eye.

Using a process called bioluminescence, the squid can light up its underside to match the surrounding light from the sun. This disguises the squid in much the same way that it discharges black ink to cloak itself. The study was recently reported in the Proceedings of the National Academies of Science.

The squid, commonly called Hawaiian Bobtail squid, has a light organ that is totally separate from the eyes. The new finding is that this organ is light sensitive and uses some of the same genes as the squid's eye.

Todd Oakley, an evolutionary biologist at UC Santa Barbara, performed the evolutionary analysis of the genes of the squid. He confirmed that the genes in the light organ are similar or the same as those of the eye of the squid.

"This is significant because it is an example of how existing components can be used in evolution to make something completely new," said Oakley. "These components existed for use in the eye and then got recruited for use in the light organ. The light organ resembles an eye in a lot of ways. It has a lens for focusing the light. It has the shape of an eye, and now we found that it has the sensitivity of an eye as well."

Oakley explained that the analogy used is "evolutionary tinkering." "Evolution acts a lot like a tinkerer and assembles what's available to make something new," he said.

The scientists gathered the small squid in shallow water in Hawaii, after sunset, when they are active. "We scoop them up with a net," said Oakley. "Then we bring them back, and keep male and female pairs together. Then they have lots of young that we can study in the lab." The squid are located in a lab at the University of Wisconsin.

"The reason that the squid are bioluminescent is for camouflage," said Oakley. "You can imagine that if you were lying on the bottom of the ocean looking up, there is a lot of light coming from above. When the squid passes over, it would cast a shadow; it would be pretty conspicuous."

To camouflage itself, the squid matches the light behind it, using bioluminescence. It matches the surrounding light so that it does not cast a shadow.

The light is caused by bacteria that are housed in the squid. It harbors the bacteria and the bacteria themselves produce the light. The scientists confirmed that the squid can actually detect the light that it is producing, by confirming that many of the genes used in the eye are also used in the light organ.

The light comes from a chemical reaction that happens within the bacteria. The squid doesn't control the chemical reaction directly, but the squid can change its light organ to make it more or less open –– to let out more or less light, Oakley explained.

A University of Colorado at Boulder team has uncovered an ancient and previously unknown Maya agricultural system -- a large manioc field intensively cultivated as a staple crop that was buried and exquisitely preserved under a blanket of ash by a volcanic eruption in present-day El Salvador 1,400 years ago.

Evidence shows the manioc field -- at least one-third the size of a football field -- was harvested just days before the eruption of the Loma Caldera volcano near San Salvador in roughly A.D. 600, said CU-Boulder anthropology Professor Payson Sheets, who is directing excavations at the ancient village of Ceren. The cultivated field of manioc was discovered adjacent to Ceren, which was buried under 17 feet of ash and is considered the best preserved ancient farming village in all of Latin America.

The ancient planting beds of the carbohydrate-rich tuber are the first and only evidence of an intensive manioc cultivation system at any New World archaeology site, said Sheets. While two isolated portions of the manioc field were discovered in 2007 following radar work and limited excavation, 18 large test pits dug in spring 2009 -- each measuring about 10 feet by 10 feet -- allowed the archaeologists to estimate the size of the field and assess the related agricultural activity that went on there.

Sheets said manioc pollen has been found at archaeological sites in Belize, Mexico and Panama, but it is not known whether it was cultivated as a major crop or was just remnants of a few garden plants. "This is the first time we have been able to see how ancient Maya grew and harvested manioc," said Sheets, who discovered Ceren in 1978.

Ash hollows in the manioc planting beds at Ceren left by decomposed plant material were cast in dental plaster by the team to preserve their shape and size, said Sheets. Evidence showed the field was harvested and then replanted with manioc stalk cuttings just a few days before the eruption of the volcano.

A few anthropologists have suspected that manioc tubers -- which can be more than three feet long and as thick as a man's arm -- were a dietary salvation for ancient, indigenous societies living in large cities in tropical Latin America. Corn, beans and squash have long been known to be staples of the ancient Maya, but they are sensitive to drought and require fertile soils, said Sheets.

"As 'high anxiety' crops, they received a lot of attention, including major roles in religious and cosmological activities of the Maya," said Sheets. "But manioc, which grows well in poor soils and is highly drought resistant did not. I like to think of manioc like an old Chevy gathering dust in the garage that doesn't get much attention, but it starts right up every time when the need arises."

Calculations by Sheets indicate the Ceren planting fields would have produced roughly 10 metric tons of manioc annually for the 100 to 200 villagers believed to have lived there. "The question now is what these people in the village were doing with all that manioc that was harvested all at once," he said. "Even if they were gorging themselves, they could not have consumed that much."

The CU-Boulder team also found the shapes and sizes of individual manioc planting ridges and walkways varied widely. "This indicates the individual farmers at Ceren had control over their families' fields and cultivated them they way they wanted, without an external higher authority telling them what to do and how to do it," he said.

The team also found that the manioc fields and adjacent cornfields at Ceren were oriented 30 degrees east of magnetic north -- the same orientation as the village buildings and the public town center, said Sheets. "The villagers laid out the agricultural fields and the town structures with the same orientation as the nearby river, showing the importance and reverence the Maya had for water," he said.

The volcano at Ceren shrouded adobe structures, thatched roofs, house beams, woven baskets, sleeping mats, garden tools and grain caches. The height of the corn stalks and other evidence indicate the eruption occurred early on an August evening, he said.Because it is unlikely that the people of Ceren were alone in their intensive cultivation of manioc, Sheets and his colleagues are now investigating chemical and microscopic botanical evidence at other Maya archaeological sites that may be indicators of manioc cultivation and processing.

Sheets said Maya villagers living in the region today have a long tradition of cutting manioc roots into small chunks, drying them eight days, then grinding the chunks into a fine, flour-like powder known as almidón. Almidón can be stored almost indefinitely, and traditionally was used by indigenous people in the region for making tamales and tortillas and as a thickening agent for stews, he said.

Since indigenous peoples in tropical South America use manioc today to brew alcoholic beverages, including beer, the CU-Boulder team will be testing ceramic vessels recovered from various structures at Ceren for traces of manioc. To date, 12 structures have been excavated, and others detected by ground-penetrating radar remain buried, he said.

Sheets is particularly interested in vessels from a religious building at Ceren excavated in 1991. The structure contained such items as a deer headdress painted red, blue and white; a large, alligator-shaped painted pot; the bones of butchered deer; and evidence that large quantities of food items like meat, corn, beans and squash were prepared on-site and dispensed to villagers from the structure, said Sheets.

Ceren's residents apparently were participating in a spiritual ceremony in the building when the volcano erupted, and did not return to their adobe homes, which excavations showed were void of people and tied shut from the outside. "I think there may have been an emergency evacuation from the ceremonial building when the volcano erupted," he said. To date, no human remains have been found at Ceren.

In a breakthrough that will help scientists unlock mysteries of the sun and its impacts on Earth, scientists have created the first-ever comprehensive computer model of sunspots. The resulting visuals capture both scientific detail and remarkable beauty. The results are published in a paper in Science Express. The research was supported by the National Science Foundation (NSF).

The high-resolution simulations of sunspots open the way for scientists to learn more about the vast mysterious dark patches on the sun's surface, first studied by Galileo. Sunspots are associated with massive ejections of charged plasma that can cause geomagnetic storms and disrupt communications and navigational systems. They are also linked to variations in solar output that can affect weather on Earth and exert a subtle influence on climate patterns.

"Understanding complexities in the solar magnetic field is key to 'space weather' forecasting," says Richard Behnke of NSF's Division of Atmospheric Sciences. "If we can model sunspots, we may be able to predict them and be better prepared for the potential serious consequences here on Earth of these violent storms on the sun."

Scientists at the National Center for Atmospheric Research (NCAR) in Boulder, Colo., collaborated with colleagues at the Max Planck Institute for Solar System Research (MPS) in Germany, building on a computer code that had been created at the University of Chicago.

"This is the first time we have a model of an entire sunspot," says lead paper author Matthias Rempel, a scientist at NCAR's High Altitude Observatory. "If you want to understand all the drivers of Earth's atmospheric system, you have to understand how sunspots emerge and evolve. Our simulations will advance research into the inner workings of the sun as well as connections between solar output and Earth's atmosphere."

Ever since outward flows from the center of sunspots were discovered 100 years ago, scientists have worked to explain the complex structure of sunspots, whose number peaks and wanes during the 11-year solar cycle. Sunspots accompany intense magnetic activity that is associated with solar flares and massive ejections of plasma that can buffet Earth's atmosphere. The resulting damage to power grids, satellites and other sensitive technological systems takes an economic toll on a rising number of industries.

Creating such detailed simulations would not have been possible even as recently as a few years ago, before the latest generation of supercomputers and a growing array of instruments to observe the sun. The new computer models capture pairs of sunspots with opposite polarity. In striking detail, they reveal the dark central region, or umbra, with brighter umbral dots, as well as webs of elongated narrow filaments with flows of mass streaming away from the spots in the outer penumbral regions. They also capture the convective flow and movement of energy that underlie the sunspots, and which are not directly detectable by instruments.

The models suggest that the magnetic fields within sunspots need to be inclined in certain directions in order to create such complex structures. The authors conclude that there is a unified physical explanation for the structure of sunspots in umbra and penumbra that's the consequence of convection in a magnetic field with varying properties.

The simulations can help scientists decipher the mysterious, subsurface forces in the sun that cause sunspots. Such work may lead to an improved understanding of variations in solar output and their impacts on Earth.

To create the simulations, the research team designed a virtual, three- dimensional domain measuring about 31,000 miles by 62,000 miles, and about 3,700 miles in depth--an expanse as long as eight times Earth's diameter, and as deep as Earth's radius.

The scientists then used a series of equations involving fundamental physical laws of energy transfer, fluid dynamics, magnetic induction and feedback, and other phenomena to simulate sunspot dynamics at 1.8 billion grid points within the domain, each spaced about 10 to 20 miles apart.

They solved the equations on NCAR's new bluefire supercomputer, an IBM machine that can perform 76 trillion calculations per second. The work drew on increasingly detailed observations from a network of ground- and space-based instruments to verify that the model captured sunspots realistically. The new models are far more detailed and realistic than previous simulations that failed to capture the complexities of the outer penumbral region.

The researchers noted, however, that even their new model does not accurately capture the lengths of the filaments in parts of the penumbra. They can refine the model by placing the grid points closer together, but that would require more computing power than is currently available.

"Advances in supercomputing power are enabling us to close in on some of the most fundamental processes of the sun," says Michael Knölker, director of NCAR's High Altitude Observatory and a co-author of the paper. "With this breakthrough simulation, an overall comprehensive physical picture is emerging for everything that observers have associated with the appearance, formation, dynamics, and the decay of sunspots on the sun's surface."

Bioengineers at Duke University have developed a laboratory robot that can successfully locate tiny pieces of metal within flesh and guide a needle to its exact location – all without the need for human assistance.

The successful proof-of-feasibility experiments lead the researchers to believe that in the future, such a robot could not only help treat shrapnel injuries on the battlefield, but might also be used for such medical procedures as placing and removing radioactive "seeds" used in the treatment of prostate and other cancers.

In their latest experiments, the engineers started with a rudimentary tabletop robot whose "eyes" are a novel 3-D ultrasound technology developed at Duke. An artificial intelligence program served as the robot's "brain" by taking the real-time 3-D information, processing it and giving the robot specific commands to perform. In their simulations, the researchers used tiny (2 millimeter) pieces of needle because, like shrapnel, they are subject to magnetism.

"We attached an electromagnet to our 3-D probe, which caused the shrapnel to vibrate just enough that its motion could be detected," said A.J. Rogers, who just completed an undergraduate degree in bioengineering at Duke. "Once the shrapnel's coordinates were established by the computer, it successfully guided a needle to the site of the shrapnel."

By proving that the robot could guide a needle to an exact location, it would simply be a matter of replacing the needle probe with a tiny tool, such as a grabber, the researchers said.

Rogers worked in the laboratory of Stephen Smith, director of the Duke University Ultrasound Transducer Group and senior member of the research team. The results of the experiments were published early online in the July issue of the journal IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control.

Since the researchers achieved positive results using a rudimentary robot and a basic artificial intelligence program, they are encouraged that simple and reasonably safe procedures will become routine in the near future as robot and artificial intelligence technology improves.

"We showed that in principle, the system works," Smith said. "It can be very difficult using conventional means to detect small pieces of shrapnel, especially in the field. The military has an extensive program of exploring the use of surgical robots in the field, and this advance could play a role."

In addition to its applications recovering the radioactive seeds used in treating prostate cancer, Smith said the system could also prove useful in removing foreign, metallic objects from the eye.

Advances in ultrasound technology have made these latest experiments possible, the researchers said, by generating detailed, 3-D moving images in real-time. The Duke team has a long track record of modifying traditional 2-D ultrasound – like that used to image babies in utero – into the more advanced 3-D scans. Since inventing the technique in 1991, the team has shown its utility by developing specialized catheters and endoscopes for real-time imaging of blood vessels in the heart and brain.

In the latest experiments, the robot successfully performed its main task: locating a tiny piece of metal in a water bath, then directing a needle on the end of the robotic arm to it. The researchers had previously used this approach to detect micro-calcifications in simulated breast tissue. In the latest experiments, Rogers added an electromagnet to the end of the transducer, or wand, the device that sends out and receives the ultrasonic waves.

"The movement caused by the electromagnet on the shrapnel was not visible to the human eye," Rogers said. "However, on the 3-D color Doppler system, the moving shrapnel stood out plainly as bright red."

The robot used in these experiments is a tabletop version capable of moving in three axes. For the next series of tests, the Duke researchers plan to use a robotic arm with six-axis capability.